Program Information
THIS IS A TEST SITE. For official annual EMP reports, please contact Sarah Perry at sarah.perry@water.ca.gov.
Water Quality monitoring is mandated by Water Right Decision 1641 for operation of the Central Valley Project (CVP) and the State Water Project (SWP). Objectives of the EMP are to document long term trends in the San Francisco Estuary and provide information for water resource management in compliance with flow-related water quality standards. The EMP is not only one of the longest estuary monitoring programs in California, but worldwide. Since 1975, and the EMP has documented long term trends for water quality, benthic invertebrates, phytoplankton, and zooplankton.
More information about EMP and its connection to the Interagency Ecological Program (IEP) can be found here.
(#fig:unnamed-chunk-2)Map of the Sacramento-San Joaquin Delta. Source: DWR
Discrete Water Quality
Background
There are 24 fixed discrete stations within the San Francisco Estuary that are monitored at high water slack tide. The stations are primarily accessed by the Research Vessel Sentinel, or vehicle transport. Discrete sampling is completed once a month due to the intensity of collecting a wide collection of physical parameters (e.g. water temperature) and grab samples for laboratory analysis (e.g. nitrogen and phosphorous). The data from the discrete sampling is helpful to document long-term changes within the estuary.
Analytes
EMP collects data on x different analytes. The ones highlighted in this report are:
- Specific Conductance
- Turbidity
- Dissolved Ammonia
- Chlorophyll a
- Dissolved Nitrate+Nitrite
- Total Phosphorus
Sites
To analyze discrete water quality trends from 2019, the EMP stations were grouped into six regions of the San Francisco Bay-Delta estuary: San Pablo Bay, Suisun and Grizzly Bay, Confluence, Central Delta, Southern Interior Delta, and Northern Interior Delta. Their locations are displayed below.
(#fig:unnamed-chunk-3)Map of EMP’s field sites.
Current Report
Introduction
Water year 2019 was classified as Above Average in the Sacramento Valley and San Joaquin Valley, unlike the previous year, which was classified as Below Average. More information about water year types can be found on the hydrology page. The 2018-2019 data from all stations within the same region were plotted on one graph and then combined with the graphs from other regions to make a facet graph for each parameter. The minimum and maximum values in 2019 were determined for each field parameter or laboratory analyte to show the range within a single year. The instances when a result fell below the reporting limit were excluded from these minimum and maximum calculations. When this occurred, a vertical dashed line capped at the reporting limit was added to the graph to represent the presence of a non-detect.
Specific Conductance
Specific conductance varied greatly in 2019 across the sampling regions with the highest levels occurring in the western regions (San Pablo Bay, Suisun Bay and Grizzly Bay and Confluence) where water from the Pacific Ocean has the strongest influence. Specific conductance ranged from 77.8 µS/cm (C10A in Southern Interior Delta, June) to 41,956 µS/cm (D41 in San Pablo Bay, November) during 2019. Lower specific conductance values were seen in 2019 than compared to 2018, which was likely due to increased precipitation and runoff during a wet year, keeping the San Francisco Estuary fresher throughout the year.
(#fig:unnamed-chunk-5)Surface specific conductance in µS/cm at six regions in the San Francisco Bay-Delta estuary during 2018-2019.
Turbidity
Turbidity values ranged from 0.3 NTU (MD10A in Southern Interior Delta, April) to 142.3 NTU (NZ325 in San Pablo Bay, February) during 2019. The year 2019 had much higher levels of turbidity than in 2018, especially during the winter months in the northern and western regions when rain and snowpack runoff occurred more frequently and to a much larger degree in the watershed. All six regions experienced a spike in turbidity in February 2019 when the first set of big storms hit, causing higher flows throughout the estuary and therefore a higher likelihood of increased sediment disturbance.
(#fig:unnamed-chunk-6)Surface turbidity in NTU at six regions in the San Francisco Bay-Delta estuary during 2018-2019.
Dissolved Ammonia
Dissolved ammonia levels in 2019 ranged from ≤ 0.05 mg/L (which is the reporting limit) to 0.75 mg/L (C3A in Northern Interior Delta, November). Dissolved ammonia levels are typically higher at C3A in the Northern Interior Delta due to its location downstream of the effluent discharge from Sacramento Regional Sanitation District. Ammonia levels are typically lower throughout the Delta and Bays, likely due to dilution and nitrification. More non-detects were seen in 2019 compared to 2018, but this was in fact due to the reporting limit increasing from 0.01 mg/L to 0.05 mg/L and was not necessarily a product of lower concentrations.
(#fig:unnamed-chunk-7)Dissolved ammonia concentrations in mg/L at six regions in the San Francisco Bay-Delta estuary during 2018-2019. Dashed lines represent the range of possible values for months where the raw value was a non-detect.
Chlorophyll a
Chlorophyll a values in 2019 ranged from ≤ 0.5 µg/L (which is the reporting limit) to 38.1 µg/L (C10A in Southern Interior Delta, July). The highest levels of chlorophyll a were seen in the Southern Interior Delta region during the summer months in 2019. This was mostly due to elevated levels at station C10A, which is known for being shallow during dry periods of the year (as low as 3.5 feet in 2019), with increased temperatures and lower flows allowing for increased phytoplankton production. These elevated chlorophyll a levels in the summer at C10A also align with the continuous fluorescence data collected at this station. More information about the phytoplankton genera is described in the phytoplankton section. Chlorophyll levels were consistently lower in 2019 than 2018 for all regions, as most regions saw a spike in chlorophyll in Spring 2018 that did not occur in 2019.
(#fig:unnamed-chunk-8)Chlorophyll a concentrations in µg/L at six regions in the San Francisco Bay-Delta estuary during 2018-2019. Dashed lines represent the range of possible values for months where the raw value was a non-detect.
Dissolved Nitrate + Nitrite
Dissolved nitrate + nitrite values ranged from ≤ 0.05 mg/L (which is the lowest reporting limit) to 3.6 mg/L (P8 in Southern Interior Delta, January) in 2019. The Southern Interior Delta region had the highest fluctuation of dissolved nitrate + nitrite concentrations and had the highest levels compared to the rest of the estuary, likely due to influence from nearby agricultural land use and wastewater treatment effluent. Most regions saw a spike in dissolved nitrate + nitrite in late 2018 to early 2019, but all regions saw less variability in 2019 compared to 2018. Reporting limits for dissolved nitrate + nitrate were as high as 7.5 and 15 mg/L for western regions in late 2019 due to chloride influence on the analytical method. These reporting limits were cropped out of graphs for scale. The dissolved nitrate + nitrite values for D4 in January and D10 in November were removed from the graphs because they were outliers.
(#fig:unnamed-chunk-9)Dissolved nitrate and nitrite concentrations in mg/L at six regions in the San Francisco Bay-Delta estuary during 2018-2019. Dashed lines represent the range of possible values for months where the raw value was a non-detect.
Total Phosphorus
In 2019, total phosphorous levels ranged from 0.04 mg/L (C3A in Northern Interior Delta-June, NZ068 in Northern Interior Delta-May, and D19 in Central Delta-May, D22 in Confluence-July) to 0.37 mg/L (P8 in Southern Interior Delta, January). Total phosphorus concentrations were similar in 2019 compared to 2018 in most regions except for the Southern Interior Delta, which experienced lower levels in 2019. This was likely due to increased precipitation and more water moving through the system causing dilution. The total phosphorus value for NZ002 in April was removed from the graph because it was an outlier.
(#fig:unnamed-chunk-10)Total phosphorous concentrations in mg/L at six regions in the San Francisco Bay-Delta estuary during 2018-2019. Dashed lines represent the range of possible values for months where the raw value was a non-detect.
Metadata
Data
EMP’s discrete water quality data sets are available publically via the Environmental Data Initiative (EDI) here.
Archived Reports
Archived annual reports can be found here (link currently broken).
Contact Information
For questions related to EMP’s discrete water quality data sets, please contact Morgan Martinez at morgan.martinez@water.ca.gov.
Benthic
Background
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Other Info
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All Sites
EMP has been collecting benthos data since 1975. The locations of all sites, current and historic, are displayed below.
(#fig:unnamed-chunk-11)Map of EMP’s benthic field sites (past and current).
Current Report
Introduction
Benthic monitoring by the Environmental Monitoring Program is conducted monthly at 10 sampling sites distributed throughout several estuarine regions from San Pablo Bay upstream through the Sacramento-San Joaquin Delta. 2019 was designated a “Wet” water year for both the Sacramento Valley and San Joaquin Valley. Benthic communities in 2019 were expected be similar to previous “Wet” years (2011 and 2017) and differ from drier years both in species composition and in species abundances.
(#fig:unnamed-chunk-12)Map of EMP’s current benthic field sites.
San Pablo Bay
The most saline of our sites, D41 and D41A, are polyhaline sites in San Pablo Bay. At D41 in 2019, the most numerous species was the non-native clam Potamocorbula amurensis, whose density peaked in July to 12,587 individuals per square meter, in a pattern seen primarily in wet years. Site D41 was also notable as the only site where we saw phoronids, also known as horseshoe worms, which are only found in this higher-salinity site.
At D41A, there were high densities of the non-native amphipod Ampelisca abdita, which had a high of 9,846 individuals/m2 in December 2019, as well as Potamocorbula amurensis with an average annual density of 1,686 individuals/m2.
(#fig:unnamed-chunk-13)Density of benthic organisms, by month, collected at station (left) D41 and (right) D41A in 2019.
Suisun and Grizzly Bay
In Suisun Bay and Grizzly Bay in 2019, our mesohaline sites D6 and D7 both saw high numbers of the invasive clam P. amurensis, which had an average density of 9,891 individuals/m2 and comprised 97% of all organisms at D6 in 2019, similar to other recent years. At D7, P. amurensis had a September peak of 12,471 individuals/m2, and the non-native amphipod Corophium alienense had a November peak of 10,428 individuals/m2. These two species together made up 94% of all organisms at D7 in 2019.
(#fig:unnamed-chunk-14)Density of benthic organisms, by month, collected at station (left) D6 and (right) D7 in 2019.
Confluence
At the confluence of the Sacramento and San Joaquin rivers, site D4’s oligohaline community was comprised in 2019 largely of the amphipods Americorophium spinicorne and Gammarus daiberi, which each had high variability through the year. The oligochaete worm Varichaetadrilus angustipenis also had high density in the second half of the year.
(#fig:unnamed-chunk-15)Density of benthic organisms, by month, collected at station D4 in 2019.
Central Delta
In the Sacramento River, freshwater site D24 was dominated by the non-native clam Corbicula fluminea, whose numbers averaged 3,016 per square meter over the course of 2019, similar to the very high densities of 2018. There was also a significant seasonal increase in densities of the amphipod Gammarus daiberi between September and December.
In the San Joaquin River, freshwater site D16 (at Twitchell Island) was dominated in 2019 by the amphipod Gammarus daiberi, which demonstrated an impressive density peak in May, as well as the clam Corbicula fluminea and the oligochaete worm V. angustipenis.
In Old River, freshwater site D28A had a diverse community in 2019. There were high densities of the ostracod crustacean Cyprideis sp. A and the sabellid worm Manayunkia speciosa at the beginning of the year and lower densities for most of the rest of 2019. There were also seasonal peaks of the oligochaete worm V. angustipenis and the amphipods G. daiberi and A. spinicorne.
(#fig:unnamed-chunk-16)Density of benthic organisms, by month, collected at station (left) D24, (center) D16 and (right) D28A in 2019.
Southern Interior Delta
Further upstream in the San Joaquin River, site P8 at Buckley Cove was dominated by the sabellid worm M. speciosa which saw peaks in October and March. In addition to this species, which accounted for 59% of all organisms, site P8 saw a diverse community of freshwater oligochaetes, aquatic insects, and amphipods in addition to the non-native clam C. fluminea.
At Clifton Court Forebay, freshwater site C9 was dominated by a number of annelid species in 2019. Varichaetadrilus angustipenis, Limnodrilus hoffmeisteri,and Ilyodrilus frantzi were present at high densities throughout the year, at moderately higher levels than in 2018. The amphipod Hyalalla sp. A experienced a dramatic peak in density in November and December (Figure 11). Site C9 is regularly one of our most biodiverse sites, with an additional large number of species present at low densities.
(#fig:unnamed-chunk-17)Density of benthic organisms, by month, collected at station (left) P8 and (right) C9 in 2019.
Summary
In summary, 2019 saw an overall decrease in invasive clam density from 2018 (13% for P. amurensis and 10% for C. fluminea). Other notable features of 2019 were the sharp decrease in overall density of the amphipod A. abdita in Grizzly Bay, after reaching a decadal peak in 2018, likely due to 2019’s decreased salinity, as well as the 2019 increase in the annelid M. speciosa, after its steady decrease from 2015 – 2018. Our ability to recognize these changes highlights the importance of monitoring benthic invertebrates to a high taxonomic resolution across the entire estuarine salinity gradient since the community has important interactions with various abiotic conditions as well as key parts of the estuarine food web.
Metadata
Data
EMP’s benthos data sets are available to download here.
Archived Reports
Archived annual reports can be found here (link currently broken).
Contact Information
For questions related to EMP’s benthos data sets, please contact Betsy Wells at elizabeth.wells@water.ca.gov.
Metadata
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